SUMMARY: Infection with HIV increases susceptibility to opportunistic infections and cancer. HIV affects not only the host immune system, but also the composition of the oral bacterial microbiome and fungal mycobiome. Moreover, the risk of oral and oropharyngeal carcinomas is increased in HIV-seropositive patients reflecting a higher rate of oral human papillomavirus (HPV) infection. Rates of HPV-associated oral papilloma have also increased as HIV-patients live longer on HAART. Based on overwhelming evidence, we postulate an etiologic association between HIV-immunosuppression, the oral microbiome / mycobiome, and HPV-associated lesions and cancer risk. We were one of the first groups to describe the complexity of the oral HPV ?virome? in HIV infected individuals. In addition, we were the first group to show increased risk of head and neck cancers with not only HPV16, but unexpectedly beta and gamma HPVs as well. These observations have profound implications for HIV-infected individuals that have a heavy burden of oral HPV infections. Moreover, we and others have reported increased diversity of the bacterial / fungal oral microbiome in HIV-infected individuals that are critical variables influencing the natural history of oral HPV in HIV-positive individuals. To further investigate these relationships using cutting edge technology, we propose to leverage the biospecimens and longitudinal data on oral HPV and risk behaviors from existing NIDCR funded studies to investigate the oral bacterial and fungal communities of HIV-positive individuals on HPV natural history. We will use Next Generation Sequencing (NGS) methods developed by our team, including metagenomics, to profile the oral bacterial (16s rRNA) and fungal (ITS1 gene) communities of oral specimens collected at repeat visits from 960 HIV-positive and HIV-negative patients followed prospectively at four institutions. Differences in the oral microbiome between individuals will be assessed with respect to HIV status, markers of HIV disease (HIV viral load, CD4 count), and oral HPV type. Associations with behavioral factors will also be assessed using available clinical data on medication use (ART and anti-biotics/-mycotics), and extensive questionnaire data on tobacco and alcohol use, sexual practices/partners, and oral hygiene. Building on existing collaborations and studies, we propose to assess the association between: (i) the oral microbiome, (ii) the oral mycobiome, and (iii) combined microbiome and mycobiome, with the natural history of oral HPV infections and lesions in HIV- positive individuals, and a HIV-negative comparison group. To the best of our knowledge, this will be the first longitudinal study to compare the oral microbiome / mycobiome and risks of oral HPV infection between HIV- infected and uninfected groups. The findings of the proposed study will provide a basis for understanding the interrelationship of HIV-related effects on the oral microbiome and mycobiome.